If you have AP and PA, then you will have to run topup to get the field map, eg, topup --imain=both.nii.gz --datain=params --config=$FSLDIR/src/topup/flirtsch/b02b0.cnf --out=out.nii.gz --fout=b0dcmap.nii.gz where both has both AP and PA and params is a file like   echo "0  1 0 1" >params   echo "0 -1 0 1" >> params consult the FSL topup page or ask them for more info

On 10/6/2022 3:20 PM, Addison, Reuben wrote:

I sent a question earlier on but I do don’t think I was clearer the first time.

I am trying to do a distortion correction using (epidewarp.fsl)

epidewarp.fsl \

--mag mag.nii.gz \

--dph dphase.nii.gz \

--tediff YOUR_TE_DIFF --esp YOUR_ESP  \

--vsm bold/b0dcmap.nii.gz

The issue we collected two field maps one in the AP direction and one in the PA direction (hence I have two different mag and phase volumes). I am not quite sure how if I should create two different maps and keep them in my bold folder for my FSFAST pipeline

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